CAM KP does not respond to any of ICEES KG-derived input CURIES

[karafecho]

This issue is to report that CAM KP does not respond to any of the ICEES KG-derived CURIES in this sheet and also appended below. Is this expected behavior? Is this a normalization issue? Is this something else?

ICEES input CURIES for MVP2 queries ExposuresProvider/cam-kp-api#81 and ExposuresProvider/cam-kp-api#82 |  
ICEES query: What chemicals are associated with primary ciliary dyskinesia? |  
[Jupyter notebook](https://colab.research.google.com/drive/1CdO0XtUddVzt5bRzlcTs8tW0SFc2ggkP#scrollTo=ZVvv2zGGsr-4&uniqifier=1)

ENTITIES_OF_INTEREST
'PUBCHEM.COMPOUND:5865',            # Prednisone |  
'CHEMBL.COMPOUND:CHEMBL1256818',    # Dextromethorphan hydrobromide |  
'PUBCHEM.COMPOUND:165363555',       # Trifacta |  
"HMDB:HMDB0252416",                 # Fluticasone |  
"PUBCHEM.COMPOUND:123600",          # Levalbuterol |  
"HMDB:HMDB0242500",                 # Budesonide |  
"CHEBI:5147",                       # Formoterol |  
"CHEMBL.COMPOUND:CHEMBL158"         # Aztreonam |  
"PUBCHEM.COMPOUND:145068"           # Nitric oxide |  
"PUBCHEM.COMPOUND:281",             # Carbon monoxide |  

[gaurav]

Thanks for this identifiers! I've added these identifiers to the brand new Automat-CAM-KP test suite (#111), and here are the results I have:

CURIE	Normalized to	How many unique CURIEs is this connected to in Automat-CAM-KP?
PUBCHEM.COMPOUND:5865	Normalized	30
CHEMBL.COMPOUND:CHEMBL1256818	PUBCHEM.COMPOUND:5462351	None
PUBCHEM.COMPOUND:165363555	Normalized	None
HMDB:HMDB0252416	PUBCHEM.COMPOUND:2462	None
PUBCHEM.COMPOUND:123600	Normalized	None
HMDB:HMDB0242500	PUBCHEM.COMPOUND:2462	None
CHEBI:5147	PUBCHEM.COMPOUND:3410	None
CHEMBL.COMPOUND:CHEMBL158	PUBCHEM.COMPOUND:5742832	9
PUBCHEM.COMPOUND:145068	Normalized	258
PUBCHEM.COMPOUND:281	Normalized	64

[gaurav]

@balhoff Do you have thoughts on figuring out how to plug in the gaps we see here in node coverage? I'm guessing we need new data sources.

[karafecho]

Thanks, @gaurav! While we don't have a 1:1 match between CURIEs, the matches that we do have are representative, with two drugs and two chemical exposures, and will allow us to move this effort along.

[karafecho]

This Swagger example query runs successfully, but it returns 0 results. If I replace the input CURIES with PUBCHEM.COMPOUND:5865 from the table above, the query also runs successfully, but it returns 0 results. I think the Automat example queries are standardized and not tailored to the underlying KGs, so perhaps you can send me an example query that returns results from CAM KP? Thanks!

{
  "message": {
    "query_graph": {
      "nodes": {
        "n0": {
          "categories": [
            "biolink:ChemicalEntity"
          ],
          "ids": [
            "CHEMBL.COMPOUND:CHEMBL3234626",
            "CHEMBL.COMPOUND:CHEMBL3234633"
          ]
        },
        "n1": {
          "categories": [
            "biolink:GeneOrGeneProduct"
          ],
          "ids": [
            "NCBIGene:2099"
          ]
        }
      },
      "edges": {
        "e01": {
          "subject": "n0",
          "object": "n1",
          "predicates": [
            "biolink:affects"
          ],
          "qualifier_constraints": [
            {
              "qualifier_set": [
                {
                  "qualifier_type_id": "biolink:object_aspect_qualifier",
                  "qualifier_value": "activity"
                },
                {
                  "qualifier_type_id": "biolink:object_direction_qualifier",
                  "qualifier_value": "increased"
                },
                {
                  "qualifier_type_id": "biolink:qualified_predicate",
                  "qualifier_value": "biolink:causes"
                }
              ]
            }
          ]
        }
      }
    }
  },
  "workflow": [
    {
      "id": "lookup"
    }
  ]
}

[gaurav]

Hi Kara! Sorry about the confusion: that Swagger example query can't currently be configured for individual platers, so we share a single Swagger with all the platers on Automat. That one isn't relevant to us, and has two main problems:

1. CAM-KP doesn't currently know about CHEMBL.COMPOUND:CHEMBL3234626 or CHEMBL.COMPOUND:CHEMBL3234633. We'd have to ingest new pathways to provide information on them. We do have information on NCBIGene:2099.
2. CAM-KP can't handle qualifiers until Generate RO-Biolink predicate mappings based on a particular Biolink model #104 has been incorporated, which we're hoping to do really soon!

So the following query will work:

{
  "message": {
    "query_graph": {
      "nodes": {
        "n0": {
          "categories": [
            "biolink:ChemicalEntity"
          ]
        },
        "n1": {
          "categories": [
            "biolink:GeneOrGeneProduct"
          ],
          "ids": [
            "NCBIGene:2099"
          ]
        }
      },
      "edges": {
        "e01": {
          "subject": "n0",
          "object": "n1",
          "predicates": [
            "biolink:affects"
          ]
        }
      }
    }
  },
  "workflow": [
    {
      "id": "lookup"
    }
  ]
}

[karafecho]

No confusion, I was aware that the Swagger examples aren't really "examples" for most of the Automats, including cam-kp and icees-kg. Thanks for an actual example query!

[karafecho]

This query returns results when sent directly to automat-icees-kg at https://automat.renci.org/#/.

{
  "message": {
    "query_graph": {
      "nodes": {
        "n0": {
          "categories": [
            "biolink:DiseaseOrPhenotypicFeature"
          ],
          "ids": [
            "MONDO:0009061"
          ]
        },
        "n1": {
          "categories": [
            "biolink:ChemicalEntity"
          ]
        }
      },
      "edges": {
        "e01": {
          "subject": "n0",
          "object": "n1",
          "predicates": [
            "biolink:correlated_with"
          ]
        }
      }
    }
  },
  "workflow": [
    {
      "id": "lookup"
    }
  ]
}

And this query returns responses when sent directly to automat-cam-kp at https://automat.renci.org/#/.

{
  "message": {
    "query_graph": {
      "nodes": {
        "n0": {
          "categories": [
            "biolink:ChemicalEntity"
          ],
          "ids": [
            "PUBCHEM.COMPOUND:5865"
          ]
        },
        "n1": {
          "categories": [
            "biolink:GeneOrGeneProduct"
          ]
        }
      },
      "edges": {
        "e01": {
          "subject": "n0",
          "object": "n1",
          "predicates": [
            "biolink:affects"
          ]
        }
      }
    }
  },
  "workflow": [
    {
      "id": "lookup"
    }
  ]
}

But this query, while able to run successfully, returns an empty response when sent to WFR at https://translator-workflow-runner.renci.org/docs#/trapi/run_workflow_query_post.

{
    "workflow": [
        {
            "id": "lookup"
        },
        {
            "id":"score"
        }
    ],
    "message": {
        "query_graph": {
            "edges": {
                "e0": {
                    "predicates": [
                        "biolink:correlated_with"
                    ],
                    "subject": "n0",
                    "object": "n1",
                    "provided_by": {
                        "allowlist": [
                            "infores:automat-icees-kg"
                        ]
                    }
                },
                "e1": {
                    "subject": "n1",
                    "object": "n2",
                    "predicates": [
                        "biolink:affects"
                    ],
                    "provided_by": {
                        "allowlist": [
                            "infores:automat-cam-kp"
                        ]
                    }
                }
            },
            "nodes": {
                "n0": {
                    "ids": [
                        "MONDO:0009061"
                    ],
                    "is_set": false
                },
                "n1": {
                    "categories": [
                        "biolink:ChemicalEntity"
                    ],
                    "is_set": false
                },
                "n2": {
                    "categories": [
                        "biolink:GeneOrGeneProduct"
                    ],
                    "is_set": false
                }
            }
        }
    }
}

[maximusunc]

This comes from going through ARAs that have strict kp timeouts vs sending queries directly to kps. I also wasn't able to get any results from the WFR, but sending directly to Aragorn with an extended timeout returns a 16.6MB response. 12k results in total. ICEES-KG took 35 seconds to respond to the first hop (normal timeout is 10s) and returned 106 results, and then CAM-KP took 90 seconds to respond with the 12k results. If you want, I can share entire response.

[karafecho]

Thanks, Max.

Given your findings, then the revised query below should run when sent to WFR and return results. However, while it runs successfully, it returns an empty KG.

{
    "workflow": [
        {
            "id": "lookup",
            "runner_parameters": {
                "allowlist": ["infores:aragorn"]
            }
        },
        {
            "id":"score"
        }
    ],
    "message": {
        "query_graph": {
            "edges": {
                "e0": {
                    "predicates": [
                        "biolink:correlated_with"
                    ],
                    "subject": "n0",
                    "object": "n1",
                    "provided_by": {
                        "allowlist": [
                            "infores:automat-icees-kg"
                        ]
                    }
                },
                "e1": {
                    "subject": "n1",
                    "object": "n2",
                    "predicates": [
                        "biolink:affects"
                    ],
                    "provided_by": {
                        "allowlist": [
                            "infores:automat-cam-kp"
                        ]
                    }
                }
            },
            "nodes": {
                "n0": {
                    "ids": [
                        "MONDO:0009061"
                    ],
                    "is_set": false
                },
                "n1": {
                    "categories": [
                        "biolink:ChemicalEntity"
                    ],
                    "is_set": false
                },
                "n2": {
                    "categories": [
                        "biolink:GeneOrGeneProduct"
                    ],
                    "is_set": false
                }
            }
        }
    }
}

[maximusunc]

Your query doesn't have the extended timeout that I'm able to set directly in Aragorn. So WFR is returning nothing because icees-kg is timed out on the first hop. This is a performance issue, and I'm only able to get results back because I can peek behind the curtain and turn some hidden knobs.

[karafecho]

Oh, I see. That makes sense.

In that case, perhaps you can send me the full response?